def file_and_status_from_metarow(self, name_and_status, read_index):
"""
['>>Sequence Length Distribution', 'pass']
"""
filename = name_and_status[0].replace(" ", "_").strip(">>") + ".csv"
filehandle = open(os.path.join(self.out_dir, read_index, filename), "w")
# new tab
if "R1" in read_index:
web_tab = WebTab([read_index, "%s/%s" % (read_index, filename)], status=name_and_status[1])
# R2; look up existing tab and add filename
else:
assert "R2" in read_index
web_tab = self.tabs[filename]
# list of lists
web_tab.filename = [web_tab.filename, [read_index, '%s/%s' % (read_index, filename)]]
# set status to worse of R1 and R2
web_tab.update_status(name_and_status[1])
return filename, filehandle, web_tab
def file_and_status_from_metarow(self, name_and_status, read_index):
"""
['>>Sequence Length Distribution', 'pass']
"""
filename = name_and_status[0].replace(" ", "_").strip(">>") + ".csv"
filehandle = open(os.path.join(self.out_dir, read_index, filename), "w")
# new tab
if read_index == "R1":
web_tab = WebTab([read_index, "R1/%s" % filename], status=name_and_status[1])
# R2; look up existing tab and add filename
else:
assert(read_index == "R2")
try:
web_tab = self.tabs[filename]
# list of lists
web_tab.filename = [web_tab.filename, ["R2", "R2/%s" % filename]]
# set status to worse of R1 and R2
web_tab.update_status(name_and_status[1])
# R2 has output that is missing from the analysis of R1
except KeyError:
# new tab, needs empty R1 plot tab
web_tab = WebTab([["R1", "R1/%s" % filename], ["R2", "R2/%s" % filename]], status=name_and_status[1])
return filename, filehandle, web_tab
def run_add(config,
name,
plot_type,
csv,
prepend=False,
status=None,
x_value=None,
y_value=None,
x_label=None,
y_label=None,
subtitle=None,
lower_quartile=None,
upper_quartile=None,
mean=None,
value=None,
label=None,
colors=None,
step=10,
min_value=None,
min_color=None,
mid_color=None,
max_value=None,
max_color=None):
"""Copies the CSV into the directory containing the config file if it does not already exist
there, then either appends an appropriate entry onto the existing config JSON or creates a new
file.
Args:
config (str): file path to config.json
name (str): name being used in the tab on the dashboard
plot_type (str): type of chart being created
csv (str): file path to data file being added to dashboard
prepend (Optional[bool]): add new plot as first tab in dashboard
status (Optional[str]): image icon to be displayed on tab [None, 'warn', 'pass', 'fail']
x_value (Optional[str]): header label in CSV containing the x-values
y_value (Optional[str]): header label in CSV containing the y-values
x_label (Optional[str]): x-label to be drawn on dashboard; defaults to `x_value`
y_label (Optional[str]): y-label to be drawn on dashboard; defaults to `y_value`
subtitle (Optional[str]): subtitle to be drawn on dashboard
lower_quartile (Optional[str]): arearange specific option; header label in CSV for lower
quartile value
upper_quartile (Optional[str]): arearange specific option; header label in CSV for upper
quartile value
mean (Optional[str]): arearange specific option; header label in CSV for mean value
value (Optional[str]): value label in CSV to be plotted in heatmap
label (Optional[str]): optional heatmap label header to mark individual coordinates
colors (Optional[str]): optional color definitions for observable labels
step (Optional[int]): histogram step
min_value (Optional[int]): optional heatmap minimum value threshold for color map
min_color (Optional[str]): optional heatmap minimum color
mid_color (Optional[str]): optional heatmap mid color for color map
max_value (Optional[int]): optional heatmap maximum value threshold for color map
max_color (Optional[str]): optional heatmap maximum color
"""
filename = add_csv_input(csv, os.path.dirname(config))
if colors:
# '(-)CTRL:#1f77b4,(+)CTRL:#d62728'
try:
colors_dict = dict([i.split(":") for i in colors.split(",")])
except ValueError:
logging.warning("Unable to parse colors (%s) in key:value pairs" %
colors)
colors_dict = None
colors = colors_dict
web_tab = WebTab(
filename, name, status,
ChartProperties(plot_type,
subtitle,
x_label,
x_value,
y_label,
y_value,
lower_quartile,
upper_quartile,
mean,
value,
label,
minimum=min_value,
maximum=max_value,
min_color=min_color,
mid_color=mid_color,
max_color=max_color,
colors=colors,
step=step))
# append onto configuration file
if os.path.exists(config):
shutil.copy(config, config + '.bak')
logging.info("Saving backup: %s" % config + '.bak')
tab_data = import_json(config)
if prepend:
tab_data.insert(0, web_tab.to_dict())
else:
tab_data.append(web_tab.to_dict())
try:
with open(config, 'w') as fh:
print(json.dumps(tab_data, indent=4), file=fh)
except Exception:
shutil.move(config + '.bak', config)
logging.exception("The backup config has been restored.")
raise
# create new
else:
with open(config, 'w') as fh:
print(json.dumps([entry], indent=4), file=fh)
logging.info("Added entry into %s\n%s" %
(config, json.dumps(web_tab.to_dict(), indent=4)))